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Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor.

Yang L, Connaris H, Potter JA, Taylor GL - BMC Struct. Biol. (2015)

Bottom Line: The domain shares the fold of other CBM40 domains that are associated with sialidases.This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions.The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK. ly10@st-andrews.ac.uk.

ABSTRACT

Background: Streptococcus pneumoniae Neuraminidase A (NanA) is a multi-domain protein anchored to the bacterial surface. Upstream of the catalytic domain of NanA is a domain that conforms to the sialic acid-recognising CBM40 family of the CAZY (carbohydrate-active enzymes) database. This domain has been identified to play a critical role in allowing the bacterium to promote adhesion and invasion of human brain microvascular endothelial cells, and hence may play a key role in promoting bacterial meningitis. In addition, the CBM40 domain has also been reported to activate host chemokines and neutrophil recruitment during infection.

Results: Crystal structures of both apo- and holo- forms of the NanA CBM40 domain (residues 121 to 305), have been determined to 1.8 Å resolution. The domain shares the fold of other CBM40 domains that are associated with sialidases. When in complex with α2,3- or α2,6-sialyllactose, the domain is shown to interact only with the terminal sialic acid. Significantly, a deep acidic pocket adjacent to the sialic acid-binding site is identified, which is occupied by a lysine from a symmetry-related molecule in the crystal. This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions.

Conclusions: The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface. The structure also suggests that small molecules or sialic acid analogues could be developed to fill the acidic pocket and hence provide a new therapeutic avenue against meningitis caused by S. pneumoniae.

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Related in: MedlinePlus

Potential functional cavity of SpCBM. a The surface electrostatic view from the top of the binding site of SpCBM and a cavity adjacent to the active site, which is occupied by a lysine from a symmetry related molecule (shown in cyan). b Close-up view of the interaction between the lysine and the protein. The solvent-accessible surface of SpCBM is coloured based on the electrostatic potential from −7 (red) to +7 (blue) kT/e, calculated using the APBS tool in PyMOL [34, 35]
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Fig6: Potential functional cavity of SpCBM. a The surface electrostatic view from the top of the binding site of SpCBM and a cavity adjacent to the active site, which is occupied by a lysine from a symmetry related molecule (shown in cyan). b Close-up view of the interaction between the lysine and the protein. The solvent-accessible surface of SpCBM is coloured based on the electrostatic potential from −7 (red) to +7 (blue) kT/e, calculated using the APBS tool in PyMOL [34, 35]

Mentions: A striking feature of the protein is a deep, negatively charged cavity adjacent to the sialic acid binding site (Fig. 6a). This pocket is formed by four residues (Glu195, Gln203, Asn207 and Asn209), and is occupied by a lysine from a symmetry-related molecule (Fig. 6b). Interestingly, a region immediately adjacent to this pocket and to the sialic acid binding site is highlighted by the results of the meta-PPISP server as a likely protein interaction site (Fig. 7). No other protein binding sites on SpCBM are predicted, and no such sites are predicted on the CBMs of NanB, NanL or NanH. NanJ CBM has a low-scoring patch in a region that overlaps with the corresponding patch on SpCBM.Fig. 6


Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor.

Yang L, Connaris H, Potter JA, Taylor GL - BMC Struct. Biol. (2015)

Potential functional cavity of SpCBM. a The surface electrostatic view from the top of the binding site of SpCBM and a cavity adjacent to the active site, which is occupied by a lysine from a symmetry related molecule (shown in cyan). b Close-up view of the interaction between the lysine and the protein. The solvent-accessible surface of SpCBM is coloured based on the electrostatic potential from −7 (red) to +7 (blue) kT/e, calculated using the APBS tool in PyMOL [34, 35]
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4546082&req=5

Fig6: Potential functional cavity of SpCBM. a The surface electrostatic view from the top of the binding site of SpCBM and a cavity adjacent to the active site, which is occupied by a lysine from a symmetry related molecule (shown in cyan). b Close-up view of the interaction between the lysine and the protein. The solvent-accessible surface of SpCBM is coloured based on the electrostatic potential from −7 (red) to +7 (blue) kT/e, calculated using the APBS tool in PyMOL [34, 35]
Mentions: A striking feature of the protein is a deep, negatively charged cavity adjacent to the sialic acid binding site (Fig. 6a). This pocket is formed by four residues (Glu195, Gln203, Asn207 and Asn209), and is occupied by a lysine from a symmetry-related molecule (Fig. 6b). Interestingly, a region immediately adjacent to this pocket and to the sialic acid binding site is highlighted by the results of the meta-PPISP server as a likely protein interaction site (Fig. 7). No other protein binding sites on SpCBM are predicted, and no such sites are predicted on the CBMs of NanB, NanL or NanH. NanJ CBM has a low-scoring patch in a region that overlaps with the corresponding patch on SpCBM.Fig. 6

Bottom Line: The domain shares the fold of other CBM40 domains that are associated with sialidases.This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions.The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, KY16 9ST, UK. ly10@st-andrews.ac.uk.

ABSTRACT

Background: Streptococcus pneumoniae Neuraminidase A (NanA) is a multi-domain protein anchored to the bacterial surface. Upstream of the catalytic domain of NanA is a domain that conforms to the sialic acid-recognising CBM40 family of the CAZY (carbohydrate-active enzymes) database. This domain has been identified to play a critical role in allowing the bacterium to promote adhesion and invasion of human brain microvascular endothelial cells, and hence may play a key role in promoting bacterial meningitis. In addition, the CBM40 domain has also been reported to activate host chemokines and neutrophil recruitment during infection.

Results: Crystal structures of both apo- and holo- forms of the NanA CBM40 domain (residues 121 to 305), have been determined to 1.8 Å resolution. The domain shares the fold of other CBM40 domains that are associated with sialidases. When in complex with α2,3- or α2,6-sialyllactose, the domain is shown to interact only with the terminal sialic acid. Significantly, a deep acidic pocket adjacent to the sialic acid-binding site is identified, which is occupied by a lysine from a symmetry-related molecule in the crystal. This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions.

Conclusions: The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface. The structure also suggests that small molecules or sialic acid analogues could be developed to fill the acidic pocket and hence provide a new therapeutic avenue against meningitis caused by S. pneumoniae.

Show MeSH
Related in: MedlinePlus